[maker-devel] MAKER annotations

[Sivaranjani Namasivayam]

Hi,

I have a query regarding MAKER predictions. I made a a first round of predictions with RNAseq data from 454 and Illumina as EST evidence and proteins sequences from related organisms as proteins evidence. I also used augustus trained on a closely related organism as the ab-initio gene predictor.
I got ~4000 maker annotations (I expect around ~10,000 genes)

I used the annotations with AED score of 0 to train SNAP and used the HMM when retraining MAKER. This time I got ~8,000 genes but when I examined some annotations they appeared to be have worsened when compared to the initial predictions: that is, genes were getting split, UTRs were not annotated and the original predictions were modified but not for better.

Would you have any suggestions on how I can improve the annotations.

Also, is there a way to tell MAKER to produce gene models for all the cufflinks assembled transcripts(that is, for the data set I provide as EST evidence).

Thanks,
Ranjani
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